Cyclodextrins: Establishing building blocks for AI-driven drug design by determining affinity constants in silico

Cyclodextrins (CDs) are cyclic carbohydrate polymers that hold significant promise for drug delivery and industrial applications. Their effectiveness depends on their ability to encapsulate target molecules with strong affinity and specificity, but quantifying affinities in these systems accurately is challenging for a variety of reasons. Computational methods represent an exceptional complement to in vitro assays because they can be employed for existing and hypothetical molecules, providing high resolution structures in addition to a mechanistic, dynamic, kinetic, and thermodynamic characterization. Here, we employ potential of mean force (PMF) calculations obtained from guided metadynamics simulations to characterize the 1:1 inclusion complexes between four different modified βCDs, with different type, number, and location of substitutions, and two sterol molecules (cholesterol and 7-ketocholesterol). Our methods, validated for reproducibility through four independent repeated simulations per system and different post processing techniques, offer new insights into the formation and stability of CD-sterol inclusion complexes. A systematic distinct orientation preference where the sterol tail projects from the CD's larger face and significant impacts of CD substitutions on binding are observed. Notably, sampling only the CD cavity's wide face during simulations yielded comparable binding energies to full-cavity sampling, but in less time and with reduced statistical uncertainty, suggesting a more efficient approach. Bridging computational methods with complex molecular interactions, our research enables predictive CD designs for diverse applications. Moreover, the high reproducibility, sensitivity, and cost-effectiveness of the studied methods pave the way for extensive studies of massive CD-ligand combinations, enabling AI algorithm training and automated molecular design.

Interactions of a Novel Anthracycline with Oligonucleotide DNA and Cyclodextrins in an Aqueous Environment

Berubicin, a chemotherapy medication belonging to the class of anthracyclines, is simulated in double-stranded DNA sequences and cyclodextrins in an aqueous environment via full-atom molecular dynamics simulations on the time scale of microseconds. The drug is studied in both the neutral and protonated states so as to better comprehend the role of its charge in the formed complexes. The noncovalent berubicin-DNA and berubicin-cyclodextrin complexes are investigated in detail, paying special attention to their thermodynamic description by employing the double decoupling method, the solvent balance method, the weighted solvent accessible surface model, and the linear interaction energy method. A novel approach for extracting the desolvation thermodynamics of the binding process is also presented. Both the binding and desolvation Gibbs energies are decomposed into entropic and enthalpic contributions so as to elucidate the nature of complexation and its driving forces. Selected structural and geometrical properties of all the complexes, which are all stable, are analyzed. Both cyclodextrins under consideration are widely utilized for drug delivery purposes, and a comparative investigation between their bound states with berubicin is carried out.

An enantioselective study of β-cyclodextrin and ionic liquid-β-cyclodextrin towards propranolol enantiomers by molecular dynamic simulations

In this study, the enantioselectivity of β-cyclodextrin and its derivatives towards propranolol enantiomers are investigated by molecular dynamic (MD) simulations. β-cyclodextrin (β-CD) have previously been shown to be able to recognize propranolol (PRP) enantiomers. To improve upon the enantioselectivity of β-cyclodextrin, we propose the use of an ionic-liquid-modified-β-cyclodextrin (β-CD-IL). β-CD-IL was found to be able to complex R and S propranolol enantiomers with differing binding energies. The molecular docking study reveals that the ionic liquid chain attached to the β-CD molecule has significant interaction with propranolol. The formation of the most stable complex occurred between (S)-β-CD-IL and (S)-propranolol with an energy of -5.80 kcal/mol. This is attributed to the formation of a hydrogen bond between the oxygen of the propranolol and the hydrogen on the primary rim of the (S)-β-CD-IL cavity. This interaction is not detected in other complexes. The root mean-squared fluctuation (RMSF) value indicates that the NH group is the most flexible molecular fragment, followed by the aromatic group. Also of note, the formation of a complex between pristine β-CD and (S)-propranolol is the least favorable.

Computational Insights into Cyclodextrin Inclusion Complexes with the Organophosphorus Flame Retardant DOPO

Cyclodextrins (CDs) were used as green char promoters in the formulation of organophosphorus flame retardants (OPFRs) for polymeric materials, and they could reduce the amount of usage of OPFRs and their release into the environment by forming [host:guest] inclusion complexes with them. Here, we report a systematic study on the inclusion complexes of natural CDs (α-, β-, and γ-CD) with a representative OPFR of DOPO using computational methods of molecular docking, molecular dynamics (MD) simulations, and quantum mechanical (QM) calculations. The binding modes and energetics of [host:guest] inclusion complexes were analyzed in details. α-CD was not able to form a complete inclusion complex with DOPO, and the center of mass distance [host:guest] distance amounted to 4-5 Å. β-CD and γ-CD allowed for a deep insertion of DOPO into their hydrophobic cavities, and DOPO was able to frequently change its orientation within the γ-CD cavity. The energy decomposition analysis based on the dispersion-corrected density functional theory (sobEDAw) indicated that electrostatic, orbital, and dispersion contributions favored [host:guest] complexation, while the exchange-repulsion term showed the opposite. This work provides an in-depth understanding of using CD inclusion complexes in OPFRs formulations.

The counteracting influence of 2-hydroxypropyl substitution and the presence of a guest molecule on the shape and size of the β-cyclodextrin cavity

The aqueous solubility of β-cyclodextrin (β-CD), a cyclic carbohydrate comprising seven α-D-glucose molecules, is enhanced by 2-hydroxypropyl (2-HP) substitution of the hydroxyl groups at the CD rims. Our thorough analysis of the structural and solvation properties with different degrees of 2-hydroxypropyl substitution on β-CD using molecular dynamics simulations reveals that the solubility is enhanced at the cost of the structural distortion of the CD cyclic structure. Substitution at the secondary rim predominantly enhances the favourable interactions between CD and water by decreasing CD-CD hydrogen bonding and promoting CD-water hydrogen bonding. However, the effect of substitution at the primary rim on the CD-water interactions is minimal; the hydrogen bonds between water and the primary hydroxyl group in native CD merely get replaced by those between water and 2-HP, since the substitution makes the primary hydroxyl oxygen (O6 atom) inaccessible to water. In contrast, substitution at the primary rim maintains the structural integrity of CD, while substitution at the secondary rim results in structural distortion due to the disruption of the intramolecular hydrogen bond belt, even leading to cavity closure. Certain strategic substitutions of the primary hydroxyl groups can help in the reduction of structural distortion, depending upon the degree of substitution at the secondary hydroxyl rim. A detailed inspection of the simulation trajectory revealed that the tilting of glucose units with the primary hydroxyl oxygen (O6) pointing inward is the primary driver for cavity closure. Even though the dynamics of glucose tilting can influence the kinetics of host-guest complex formation, once the guest is well incorporated into the cavity, glucose tilting is inhibited and the cavity opens up as in native β-CD.

Solvent effects in anion recognition

Anion recognition is pertinent to a range of environmental, medicinal and industrial applications. Recent progress in the field has relied on advances in synthetic host design to afford a broad range of potent recognition motifs and novel supramolecular structures capable of effective binding both in solution and at derived molecular films. However, performance in aqueous media remains a critical challenge. Understanding the effects of bulk and local solvent on anion recognition by host scaffolds is imperative if effective and selective detection in real-world media is to be viable. This Review seeks to provide a framework within which these effects can be considered both experimentally and theoretically. We highlight proposed models for solvation effects on anion binding and discuss approaches to retain strong anion binding in highly competitive (polar) solvents. The synthetic design principles for exploiting the aforementioned solvent effects are explored.

Molecular dynamics simulation techniques and their application to aroma compounds/cyclodextrin inclusion complexes: A review

Homeostatic technologies play a crucial role in maintaining the quality and extending the service life of aroma compounds (ACs). Commercial cyclodextrins (CDs) are commonly used to form inclusion complexes (ICs) with ACs to enhance their solubility, stability, and morphology. The selection of suitable CDs and ACs is of paramount importance in this process. Molecular dynamics (MD) simulations provide an in-depth understanding of the interactions between ACs and CDs, aiding researchers in optimising the properties and effects of ICs. This review offers a systematic discussion of the application of MD simulations in ACs/CDs ICs, covering the establishment of the simulation process, parameter selection, model evaluation, and various application cases, along with their advantages and disadvantages. Additionally, this review summarises the major achievements and challenges of this method while identifying areas that require further exploration. These findings may contribute to a comprehensive understanding of the formation and stabilization mechanisms of ACs/CDs ICs and offer guidance for the selection and computational characterisation of CDs in the AC steady state.

QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations

Understanding the interaction of ligands with biomolecules is an integral component of drug discovery and development. Challenges for computing thermodynamic and kinetic quantities for pharmaceutically relevant receptor-ligand complexes include the size and flexibility of the ligands, large-scale conformational rearrangements of the receptor, accurate force field parameters, simulation efficiency, and sufficient sampling associated with rare events. Our recently developed multiscale milestoning simulation approach, SEEKR2 (Simulation Enabled Estimation of Kinetic Rates v.2), has demonstrated success in predicting unbinding (koff) kinetics by employing molecular dynamics (MD) simulations in regions closer to the binding site. The MD region is further subdivided into smaller Voronoi tessellations to improve the simulation efficiency and parallelization. To date, all MD simulations are run using general molecular mechanics (MM) force fields. The accuracy of calculations can be further improved by incorporating quantum mechanical (QM) methods into generating system-specific force fields through reparameterizing ligand partial charges in the bound state. The force field reparameterization process modifies the potential energy landscape of the bimolecular complex, enabling a more accurate representation of the intermolecular interactions and polarization effects at the bound state. We present QMrebind (Quantum Mechanical force field reparameterization at the receptor-ligand binding site), an ORCA-based software that facilitates reparameterizing the potential energy function within the phase space representing the bound state in a receptor-ligand complex. With SEEKR2 koff estimates and experimentally determined kinetic rates, we compare and interpret the receptor-ligand unbinding kinetics obtained using the newly reparameterized force fields for model host-guest systems and HSP90-inhibitor complexes. This method provides an opportunity to achieve higher accuracy in predicting receptor-ligand koff rate constants.

Enabling Stereochemical Communication and Stimuli-Responsive Chiroptical Properties in Biphenyl-Capped Cyclodextrins

Chiroptical materials are gaining increasing interest due to their innovative character and their applications in optoelectronics and data encryption technologies. Fully harnessing the potential of building blocks from the "chiral pool", such as native cyclodextrins (CDs), as they often lack chromophores suitable for the construction of materials with significant chiroptical properties. Here, we present the synthesis and characterization of a two-level molecular stack consisting of a point-chiral element (CD) and an axially chiral element (biphenyl), capable of effectively translating the overall stereochemical information contained in CDs into stimuli-responsive chiroptical properties. α- and β-permethylated CDs were efficiently capped with two different 2,2'-difunctionalized 1,1'-biphenyl units. In CD derivatives containing the rigid 2,2'-dihydroxy-1,1'-biphenyl cap, two intramolecular hydrogen bonds act synergistically as stereoselective actuators, enabling effective communication between the two levels and the transfer of nonchromophoric stereochemical information from the cyclic-oligosaccharide to the atropoisomeric cap. The chiroptical properties can be finely tuned by external stimuli such as temperature and solvent. The way chirality is transferred from the CD platform to the biphenyl cap was revealed thanks to crystallographic and computational analyses, together with electronic circular dichroism (ECD) studies.

Liquid Structure Scenario of the Archetypal Supramolecular Deep Eutectic Solvent: Heptakis(2,6-di-O-methyl)-β-cyclodextrin/levulinic Acid

The concept of supramolecular solvents has been recently introduced, and the extended liquid-state window accessible for mixtures of functionalized cyclodextrins (CDs) with hydrogen bond (HB) donor species, e.g., levulinic acid, led to the debut of supramolecular deep eutectic solvents (SUPRA-DES). These solvents retain CD's inclusion ability and complement it with enhanced solvation effectiveness due to an extended HB network. However, so far, these promising features were not rationalized in terms of a microscopic description, thus hindering a more complete capitalization. This is the first joint experimental and computational study on the archetypal SUPRA-DES: heptakis(2,6-di-O-methyl)-β-CD/levulinic acid (1:27). We used X-ray scattering to probe CD's aggregation level and molecular dynamics simulation to determine the nature of interactions between SUPRA-DES components. We discover that CDs are homogeneously distributed in bulk and that HB interactions, together with the electrostatic ones, play a major role in determining mutual interaction between components. However, dispersive forces act in synergy with HB to accomplish a fundamental task in hindering hydrophobic interactions between neighbor CDs and maintaining the system homogeneity. The mechanism of mutual solvation of CD and levulinic acid is fully described, providing fundamental indications on how to extend the spectrum of SUPRA-DES combinations. Overall, this study provides the key to interpreting structural organization and solvation tunability in SUPRA-DES to extend the range of sustainable applications for these new, unique solvents.

Insights from molecular dynamics and DFT calculations into the interaction of 1,4-benzodiazepines with 2-hydroxypropyl-βCD in a theoretical study

This study delves into the interaction between benzodiazepine (BZD) drugs and 2-hydroxypropyl-β-cyclodextrin (2HPβCD), a cyclodextrin (CD) known to improve drug delivery and enhance therapeutic outcomes. We find that the 2HPβCD's atoms become more rigid in the presence of chlordiazepoxide (CDP), clonazepam (CLZ), and diazepam (DZM), whereas they become more flexible in the presence of nordazepam (NDM) and nitrazepam (NZP). We also investigated the structure of 2HPβCD and found that loading these drugs increases both the area and volume of the 2HPβCD cavity, making it more suitable for drug delivery. Moreover, this research found that all drugs exhibited negative values for the binding free energy, indicating thermodynamic favorability and improved solubility. The binding free energy order of the BZDs was consistent in both molecular dynamics and Monte Carlo methods, with CDP and DZM having the highest affinity for binding. We also analyzed the contribution of different interaction energies in binding between the carrier and the drugs and found that Van der Waals energy is the primary component. Our results indicate that the number of hydrogen bonds between 2HPβCD/water slightly decreases in the presence of BZDs, but the hydrogen bond's quality remains constant.

How are N-methylcarbamates encapsulated by β-cyclodextrin: insight into the binding mechanism

Guest molecules containing chromophore groups encapsulated by β-cyclodextrin (β-CD) generate circular dichroism (CD) signals, which enables a preliminary prediction of their binding modes. However, the accurate determination of the representative binding conformation (RC) remains a challenging task due to the complex conformational space of these host-guest systems. Here, we combine a molecular dynamics/quantum mechanics/continuum solvent model (MD/QM/CSM) with induced circular dichroism (ICD) data (N. L. Pacioni, A. B. Pierini and A. V. Veglia, Spectrochim. Acta A Mol. Biomol. Spectrosc., 2013, 103, 319-324.) to explore the binding mechanism of β-CD with four N-methylcarbamate molecules: promecarb (PC), bendiocarb (BC), carbaryl (CY) and carbofuran (CF). In aqueous solution, their stability decreases as: PC > BC > CY > CF. Comparing the ECD spectra computed from TD-DFT with the ICD data can help eliminate many common binding configurations and identify the RC. The host-guest binding affinities (BAs) estimated using a ONIOM2(B971:PM6)/SMD model reproduce the measured binding trend, reveal the competition between the non-covalent interaction and solvent effect and explain the large difference in their binding modes. We also examine the fluctuations in the computed BA using similar structures.

Evaluation of polyanionic cyclodextrins as high affinity binding scaffolds for fentanyl

Cyclodextrins (CDs) have been previously shown to display modest equilibrium binding affinities (K_a ~ 100-200 M^-1) for the synthetic opioid analgesic fentanyl. In this work, we describe the synthesis of new CDs possessing extended thioalkylcarboxyl or thioalkylhydroxyl moieties and assess their binding affinity towards fentanyl hydrochloride. The optimal CD studied displays a remarkable affinity for the opioid of K_a = 66,500 M^-1, the largest value reported for such an inclusion complex to date. One dimensional ¹H Nuclear Magnetic Resonance (NMR) as well as Rotational Frame Overhauser Spectroscopy (2D-ROESY) experiments supported by molecular dynamics (MD) simulations suggest an unexpected binding behavior, with fentanyl able to bind the CD interior in one of two distinct orientations. Binding energies derived from the MD simulations work correlate strongly with NMR-derived affinities highlighting its utility as a predictive tool for CD candidate optimization. The performance of these host molecules portends their utility as platforms for medical countermeasures for opioid exposure, as biosensors, and in other forensic science applications.

Structural Studies of Piperine Inclusion Complexes in Native and Derivative β-Cyclodextrins

Piperine (PN), the primary pungent alkaloid in black pepper shows several biological activities such as antioxidant, antimicrobial and anti-cancerogenic effects. Similar to other alkaloids, PN is characterized by poor water solubility. One way to improve its solubility and thus its biological activities is by forming inclusion complexes with suitable cyclodextrins. In this work PN inclusion complexes in native β-cyclodextrin (β-CD), its methylated (randomly methylated (RM-β-CD), heptakis-(2,6-di-O-methyl)-β-CD (DM-β-CD) and heptakis-(2,3,6-tri-O-methyl)-β-CD (TM-β-CD)) and 2-hydroxypropylated (HP-β-CD) derivatives are investigated using physicochemical methods, such as phase solubility study and X-ray crystallography complemented by theoretical (molecular dynamics simulations) studies. The determination of the crystal structure of the PN inclusion complexes in β-CD, DM-β-CD and TM-β-CD, reveals the formation of 1:2 guest:host inclusion complexes in the crystalline state. The guest PN molecule threads the hydrophobic cavities of the hosts which are arranged as couples in a tail-to-tail mode in the case of PN/β-CD and in a head-to-tail mode in the cases of PN/DM-β-CD and PN/TM-β-CD. MD studies based on the crystallographically determined structures and docked models show the stability of the examined complexes in an aqueous environment whereas the binding affinity of PN for the host molecules is calculated by the MM/GBSA method. Finally, phase-solubility studies of PN with β-CD, RM-β-CD and HP-β-CD are presented, indicating a B_s-type for the PN/β-CD complex and an A_L-type for the PN/RM-β-CD and PN/HP-β-CD complexes with 1:1 guest:host stoichiometry.

Molecular Symmetry of Permethylated β-Cyclodextrins upon Complexation

The Cn molecular symmetry implicated by the schemes with which cyclodextrins (CDs), the well-known cyclic oligosaccharides, are introduced in the literature, is not valid. Numerous studies have shown that CDs are rather flexible with their macrocycle adopting various conformations that enable the inclusion complexation of guest molecules of various shapes. In this work, the loss and gain of the C7 symmetry of the heptakis (2, 3, 6-tri-O-methyl)-β-CD (TM-β-CD) is investigated by means of its conformation geometrical features in its hydrated form and upon complexation with molecules of different shapes. For this, the crystal structure of the inclusion complex of a bulky guest molecule (giberellic acid) in TM-β-CD is presented for the first time and compared with the previously determined crystal structures of monohydrated TM-β-CD and the inclusion complex of a linear monoterpenoid (geraniol) in TM-β-CD. The structural investigation was complemented by molecular dynamics simulations in an explicit solvent, based on the crystallographically determined models. The crucial role of the guest, in the symmetry gain of the host, reveals a pronounced induced-fit complexation mechanism for permethylated CDs.

Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective

The dissociation rate (k off) associated with ligand unbinding events from proteins is a parameter of fundamental importance in drug design. Here we review recent major advancements in molecular simulation methodologies for the prediction of k off. Next, we discuss the impact of the potential energy function models on the accuracy of calculated k off values. Finally, we provide a perspective from high-performance computing and machine learning which might help improve such predictions.

Solubility of Hydrophobes into Macrocyclic Hosts

The intrinsic nature of macrocyclic molecules to preferentially absorb a specific solute has been opening up supramolecular chemistry. Nevertheless, the determinant factor with molecular perspectives in promoting host-guest complexations remains inconclusive, due to the lack of rigorous thermodynamic examination on the guest solubility inside the host. Here, we quantify the solute-solvent energetic and entropic contributions between the end states and on the docking route during inclusion of noble gases in cucurbit[5]uril, cucurbit[6]uril, and α-cyclodextrin, using molecular dynamics simulations in combination with the potential distribution theorem. Results show that in all of the pairs examined both the solute-solvent energy and entropy favor the inclusion, while the former is rather dominant. The frequency of interior drying, which pertains to the entropic contribution, differs between the hosts and is controlled by the existence of lid water at portal and the flexibility of host framework. Moreover, the hosts exhibit various types of absorption manners, involving non-, single-, and double-free-energy barriers.

Biophysical Studies and In Vitro Effects of Tumor Cell Lines of Cannabidiol and Its Cyclodextrin Inclusion Complexes

Phytocannabinoids possess anticancer properties, as established in vitro and in vivo. However, they are characterized by high lipophilicity. To improve the properties of cannabidiol (CBD), such as solubility, stability, and bioavailability, CBD inclusion complexes with cyclodextrins (CDs) might be employed, offering targeted, faster, and prolonged CBD release. The aim of the present study is to investigate the in vitro effects of CBD and its inclusion complexes in randomly methylated β-CD (RM-β-CD) and 2-hyroxypropyl-β-CD (HP-β-CD). The enhanced solubility of CBD upon complexation with CDs was examined by phase solubility study, and the structure of the inclusion complexes of CBD in 2,6-di-O-methyl-β-CD (DM-β-CD) and 2,3,6-tri-O-methyl-β-CD (TM-β-CD) was determined by X-ray crystallography. The structural investigation was complemented by molecular dynamics simulations. The cytotoxicity of CBD and its complexes with RM-β-CD and HP-β-CD was tested on two cell lines, the A172 glioblastoma and TE671 rhabdomyosarcoma cell lines. Methylated β-CDs exhibited the best inclusion ability for CBD. A dose-dependent effect of CBD on both cancer cell lines and improved efficacy of the CBD–CDs complexes were verified. Thus, cannabinoids may be considered in future clinical trials beyond their palliative use as possible inhibitors of cancer growth.

An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica

The effect of immobilized $$\upbeta$$ β -cyclodextrin (bCD) molecules inside a mesoporous silica support on the uptake of benzene and p-nitrophenol from aqueous solution was investigated using all-atom molecular dynamics (MD) simulations. The calculated adsorption isotherms are discussed with respect to the free energies of binding for a 1:1 complex of bCD and the aromatic guest molecule. The adsorption capacity of the bCD-containing material significantly exceeds the amount corresponding to a 1:1 binding scenario, in agreement with experimental observations. Beside the formation of 1:2 and, to a lesser extent, 1:3 host:guest complexes, also host–host interactions on the surface as well as more unspecific host–guest interactions govern the adsorption process. The demonstrated feasibility of classical all-atom MD simulations to calculate liquid phase adsorption isotherms paves the way to a molecular interpretation of experimental data that are too complex to be described by empirical models.

Measurement of Single-Molecule Forces in Cholesterol and Cyclodextrin Host-Guest Complexes

Biological host molecules such as β-cyclodextrins (β-CDs) have been used to remove cholesterol guests from membranes and artery plaques. In this work, we calibrated the host-guest intermolecular mechanical forces (IMMFs) between cholesterol and cyclodextrin complexes by combining single-molecule force spectroscopy in optical tweezers and computational molecular simulations for the first time. Compared to native β-CD, methylated beta cyclodextrins complexed with cholesterols demonstrated higher mechanical stabilities due to the loss of more high-energy water molecules inside the methylated β-CD cavities. This result is consistent with the finding that methylated β-CD is more potent at solubilizing cholesterols than β-CD, suggesting that the IMMF can serve as a novel indicator to evaluate the solubility of small molecules such as cholesterols. Importantly, we found that the force spectroscopy measured in such biological host-guest complexes is direction-dependent: pulling from the alkyl end of the cholesterol molecule resulted in a larger IMMF than that from the hydroxyl end of the cholesterol molecule. Molecular dynamics coupled with umbrella sampling simulations further revealed that cholesterol molecules tend to enter or leave from the wide opening of cyclodextrins. Such an orientation rationalizes that cyclodextrins are rather efficient at extracting cholesterols from the phospholipid bilayer in which hydroxyl groups of cholesterols are readily exposed to the hydrophobic cavities of cyclodextrins. We anticipate that the IMMF measured by both experimental and computational force spectroscopy measurements help elucidate solubility mechanisms not only for cholesterols in different environments but also to host-guest systems in general, which have been widely exploited for their solubilization properties in drug delivery, for example.

Application of Molecular Dynamics Simulations in the Analysis of Cyclodextrin Complexes

Cyclodextrins (CDs) are highly respected for their ability to form inclusion complexes via host-guest noncovalent interactions and, thus, ensofance other molecular properties. Various molecular modeling methods have found their applications in the analysis of those complexes. However, as showed in this review, molecular dynamics (MD) simulations could provide the information unobtainable by any other means. It is therefore not surprising that published works on MD simulations used in this field have rapidly increased since the early 2010s. This review provides an overview of the successful applications of MD simulations in the studies on CD complexes. Information that is crucial for MD simulations, such as application of force fields, the length of the simulation, or solvent treatment method, are thoroughly discussed. Therefore, this work can serve as a guide to properly set up such calculations and analyze their results.

Evaluating the Performance of Water Models with Host-Guest Force Fields in Binding Enthalpy Calculations for Cucurbit[7]uril-Guest Systems

Computational prediction of thermodynamic components with computational methods has become increasingly routine in computer-aided drug design. Although there has been significant recent effort and improvements in the calculation of free energy, the prediction of enthalpy (and entropy) remains underexplored. Furthermore, there has been relatively little work reported so far that attempts to comparatively assess how well different force fields and water models perform in conjunction with each other. Here, we report a comprehensive assessment of force fields and water models using host-guest systems that mimic many features of protein-ligand systems. These systems are computationally inexpensive, possibly because of their small size compared to protein-ligand systems. We present absolute enthalpy calculations using the multibox approach on a set of 25 cucurbit[7]uril-guest pairs. Eight water models were considered (TIP3P, TIP4P, TIP4P-Ew, SPC, SPC/E, OPC, TIP5P, Bind3P), along with five force fields commonly used in the literature (GAFFv1, GAFFv2, CGenFF, Parsley, and SwissParam). We observe that host-guest binding enthalpies are strongly sensitive to the selection of force field and water model. In terms of water models, we find that TIP3P and its derivative Bind3P are the best performing models for this particular host-guest system. The performance is generally better for aliphatic compounds than for aromatic ones, suggesting that aromaticity remains a difficult property to include accurately in these simple force fields.

Diffusivity of α-, β-, γ-cyclodextrin and the inclusion complex of β-cyclodextrin: Ibuprofen in aqueous solutions; A molecular dynamics simulation study

Cyclodextrins (CDs) are widely used in drug delivery, catalysis, food and separation processes. In this work, a comprehensive simulation study on the diffusion of the native α-, β- and γ-CDs in aqueous solutions is carried out using Molecular Dynamics simulations. The effect of the system size on the computed self-diffusivity is investigated and it is found that the required correction can be as much as 75% of the final value. The effect of the water force field is examined and it is shown that the q4md-CD/TIP4P/2005 force field combination predicts the experimentally measured self-diffusion coefficients of CDs very accurately. The self-diffusion coefficients of the three native CDs were also computed in aqueous-NaCl solutions using the Joung and Cheatham (JC) and the Madrid-2019 force fields. It is found that Na+ ions have higher affinity towards the CDs when the JC force field is used and for this reason the predicted diffusivity of CDs is lower compared to simulations using the Madrid-2019 force field. As a model system for drug delivery and waste-water treatment applications, the diffusion of the β-CD:Ibuprofen inclusion complex in water is studied. In agreement with experiments for similar components, it is shown that the inclusion complex and the free β-CD have almost equal self-diffusion coefficients. Our analysis revealed that this is most likely caused by the almost full inclusion of the ibuprofen in the cavity of the β-CD. Our findings show that Molecular Dynamics simulation can be used to provide reasonable diffusivity predictions, and to obtain molecular-level understanding useful for industrial applications of CDs.

Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-Based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization

We present Swarm-CG, a versatile software for the automatic iterative parametrization of bonded parameters in coarse-grained (CG) models, ideal in combination with popular CG force fields such as MARTINI. By coupling fuzzy self-tuning particle swarm optimization to Boltzmann inversion, Swarm-CG performs accurate bottom-up parametrization of bonded terms in CG models composed of up to 200 pseudo atoms within 4-24 h on standard desktop machines, using default settings. The software benefits from a user-friendly interface and two different usage modes (default and advanced). We particularly expect Swarm-CG to support and facilitate the development of new CG models for the study of complex molecular systems interesting for bio- and nanotechnology. Excellent performances are demonstrated using a benchmark of 9 molecules of diverse nature, structural complexity, and size. Swarm-CG is available with all its dependencies via the Python Package Index (PIP package: swarm-cg). Demonstration data are available at: www.github.com/GMPavanLab/SwarmCG.

Ranking of Ligand Binding Kinetics Using a Weighted Ensemble Approach and Comparison with a Multiscale Milestoning Approach

To improve lead optimization efforts in finding the right ligand, pharmaceutical industries need to know the ligand's binding kinetics, such as binding and unbinding rate constants, which often correlate with the ligand's efficacy in vivo. To predict binding kinetics efficiently, enhanced sampling methods, such as milestoning and the weighted ensemble (WE) method, have been used in molecular dynamics (MD) simulations of these systems. However, a comparison of these enhanced sampling methods in ranking ligands has not been done. Hence, a WE approach called the concurrent adaptive sampling (CAS) algorithm that uses MD simulations was used to rank seven ligands for β-cyclodextrin, a system in which a multiscale milestoning approach called simulation enabled estimation of kinetic rates (SEEKR) was also used, which uses both MD and Brownian dynamics simulations. Overall, the CAS algorithm can successfully rank ligands using the unbinding rate constant k_off values and binding free energy ΔG values, as SEEKR did, with reduced computational cost that is about the same as SEEKR. We compare the CAS algorithm simulations with different parameters and discuss the impact of parameters in ranking ligands and obtaining rate constant and binding free energy estimates. We also discuss similarities and differences and advantages and disadvantages of SEEKR and the CAS algorithm for future use.

Molecular View into the Cyclodextrin Cavity: Structure and Hydration

We find, through atomistic molecular dynamics simulation of native cyclodextrins (CDs) in water, that although the outer surface of a CD appears like a truncated cone, the inner cavity resembles a conical hourglass because of the inward protrusion of the glycosidic oxygens. Furthermore, the conformations of the constituent α-glucose molecules are found to differ significantly from a free monomeric α-glucose molecule. This is the first computational study that maps the conformational change to the preferential hydrogen bond donating capacity of one of the secondary hydroxyl groups of CD, in consensus with an NMR experiment. We have developed a simple and novel geometry-based technique to identify water molecules occupying the nonspherical CD cavity, and the computed water occupancies are in close agreement with the experimental and density functional theory studies. Our analysis reveals that a water molecule in CD cavity loses out about two hydrogen bonds and remains energetically frustrated but possesses higher orientational degree of freedom compared to bulk water. In the context of CD-drug complexation, these imply a nonclassical, that is, enthalpically driven hydrophobic association of a drug in CD cavity.

Cyclodextrin complexation studies as the first step for repurposing of chlorpromazine

The antipsychotic drug chlorpromazine (CPZ) has potential for the treatment of acute myeloid leukemia, if central nervous system side-effects resulting from its passage through the blood-brain barrier can be prevented. A robust drug delivery system for repurposed CPZ would be drug-in-cyclodextrin-in-liposome that would redirect the drug away from the brain while avoiding premature release in the circulation. As a first step, CPZ complexation with cyclodextrin (CD) has been studied. The stoichiometry, binding constant, enthalpy, and entropy of complex formation between CPZ and a panel of CDs was investigated by isothermal titration calorimetry (ITC). All the tested CDs were able to include CPZ, in the form of 1:1, 1:2 or a mixture of 1:1 and 1:2 complexes. In particular, a substituted γ-CD, sugammadex (the octasodium salt of octakis(6-deoxy-6-S-(2-carboxyethyl)-6-thio)cyclomaltooctaose), formed exclusively 1:2 complexes with an extremely high association constant of 6.37 × 10⁹ M^-2. Complexes were further characterized by heat capacity changes, one- and two-dimensional (ROESY) nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics simulations. Finally, protection of CPZ against photodegradation by CDs was assessed. This was accelerated rather than reduced by complexation with CD. Altogether these results provide a molecular basis for the use of CD in delayed release formulations for CPZ.

Inclusion Complexation of Organic Micropollutants with β-Cyclodextrin

Recently, β-cyclodextrin (βCD)-based polymers with enhanced adsorption kinetics and high removal capacity of organic micropollutants (OMPs) and uptake rates have been synthesized and tested experimentally. Although the exact physical–chemical mechanisms via which these polymers capture the various types of OMPs are not yet fully understood, it is suggested that the inclusion complex formation of OMPs with βCD is very important. In this study, the inclusion complex formation of OMPs with βCD in an aqueous solution is investigated by using the well-established attach–pull–release method in force field-based molecular dynamics simulations. A representative set of OMPs is selected based on the measured occurrences in surface and ground waters and the directives published by the European Union. To characterize the formation of the inclusion complex, the binding free energies, enthalpies, and entropies are computed and compared to experimental values. It is shown that computations using the q4md-CD/GAFF/Bind3P force field combination yield binding free energies that are in reasonable agreement with the experimental results for all OMPs studied. The binding enthalpies are decomposed into the main contributing interaction types. It is shown that, for all studied OMPs, the van der Waals interactions are favorable for the inclusion complexion and the hydrogen bond formation of the guest with the solvent and βCD plays a crucial role in the binding mechanism. Our findings show that MD simulations can adequately describe the inclusion complex formation of βCD with OMPs, which is the first step toward understanding the underlying mechanisms via which the βCD-based polymers capture OMPs.

Inclusion Complexes of Naringenin in Dimethylated and Permethylated β-Cyclodextrins: Crystal Structures and Molecular Dynamics Studies

The crystal structures of the inclusion complexes of naringenin in dimethylated and permethylated β-cyclodextrin (DM-β-CD and TM-β-CD) were determined and extensively analyzed. Naringenin is found with its 4-hydroxyphenyl residue fully immersed in the DM-β-CD cavity and its chromone group protruding from the narrow rim of the open-cone shaped host. The naringenin/DM-β-CD complex units are packed in a ‘herring bone’ fashion. In the case of naringenin/TM-β-CD, the complex units are arranged in a cage-type mode, the guest naringenin is partially encapsulated in the cavity of the closed-cone shaped host, with its chromone group laying equatorially and its 4-hydroxyphenyl protruding extensively from the wide rim of the host. Furthermore, the crystallographically-determined coordinates of both complexes were employed for Molecular Dynaimics simulations in explicit water solvent and in the absence of crystal contacts. The trajectories showed that naringenin rapidly penetrates the open narrow rim of DM-β-CD but not the closed narrow rim of TM-β-CD. Thus, in the latter case, the chromone group of naringenin is accommodated shallowly in the wide rim of the host, tethered via hydrogen bonds to the secondary methoxy groups of the host. Finally, a significantly higher binding affinity for naringenin in DM-β-CD than TM-β-CD was estimated by Molecular Mechanics/Generalized Born Surface Area calculations.

Binding Thermodynamics of Host-Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative

Designing ligands that bind their target biomolecules with high affinity and specificity is a key step in small-molecule drug discovery, but accurately predicting protein-ligand binding free energies remains challenging. Key sources of errors in the calculations include inadequate sampling of conformational space, ambiguous protonation states, and errors in force fields. Noncovalent complexes between a host molecule with a binding cavity and a druglike guest molecule have emerged as powerful model systems. As model systems, host-guest complexes reduce many of the errors in more complex protein-ligand binding systems, as their small size greatly facilitates conformational sampling, and one can choose systems that avoid ambiguities in protonation states. These features, combined with their ease of experimental characterization, make host-guest systems ideal model systems to test and ultimately optimize force fields in the context of binding thermodynamics calculations. The Open Force Field Initiative aims to create a modern, open software infrastructure for automatically generating and assessing force fields using data sets. The first force field to arise out of this effort, named SMIRNOFF99Frosst, has approximately one tenth the number of parameters, in version 1.0.5, compared to typical general small molecule force fields, such as GAFF. Here, we evaluate the accuracy of this initial force field, using free energy calculations of 43 α and β-cyclodextrin host-guest pairs for which experimental thermodynamic data are available, and compare with matched calculations using two versions of GAFF. For all three force fields, we used TIP3P water and AM1-BCC charges. The calculations are performed using the attach-pull-release (APR) method as implemented in the open source package, pAPRika. For binding free energies, the root-mean-square error of the SMIRNOFF99Frosst calculations relative to experiment is 0.9 [0.7, 1.1] kcal/mol, while the corresponding results for GAFF 1.7 and GAFF 2.1 are 0.9 [0.7, 1.1] kcal/mol and 1.7 [1.5, 1.9] kcal/mol, respectively, with 95% confidence ranges in brackets. These results suggest that SMIRNOFF99Frosst performs competitively with existing small molecule force fields and is a parsimonious starting point for optimization.

Direct and Regioselective Di-α-fucosylation on the Secondary Rim of β-Cyclodextrin

A straightforward glycosylation method is described to regio- and stereoselectively introduce two α-l-fucose moieties directly to the secondary rim of β-cyclodextrin. Using NMR and MS fragmentation studies, the nonasaccharide structure was determined, which was also visualized using molecular dynamics simulations. The reported glycosylation method proved to be robust on gram-scale, and may be generally applied to directly glycosylate β-cyclodextrins to make well-defined multivalent glycoclusters.

Functional self-assembled nanovesicles based on β-cyclodextrin, liposomes and adamantyl guanidines as potential nonviral gene delivery vectors

Multicomponent self-assembled supramolecular nanovesicles based on an amphiphilic derivative of β-cyclodextrin and phosphatidylcholine liposomes (PC-liposomes) functionalized with four structurally different adamantyl guanidines were prepared and characterized. Incorporation efficiency of the examined adamantyl guanidines as well as size and surface charge of the prepared supramolecular nanovesicles was determined. Changes in the surface charge of the prepared nanovesicles confirmed that guanidinium groups were exposed on the surface. ITC and 1H NMR spectroscopy complemented by molecular dynamics (MD) simulations were used to elucidate the structural data and stability of the inclusion complexes of β-cyclodextrin and adamantyl guanidines (AG1-5). The results are consistent and point to a significant contribution of the guanylhydrazone residue to the complexation process for AG1 and AG2 with β-cyclodextrin. In order to evaluate the potential of the self-assembled supramolecular nanomaterial as a nonviral gene delivery vector, fluorescence correlation spectroscopy was used. It showed that the prepared nanovesicles functionalized with adamantyl guanidines AG1-4 effectively recognize and bind the fluorescently labelled DNA. Furthermore, gel electrophoretic assay confirmed the formation of nanoplexes of functionalized nanovesicles and plasmid DNA. These findings together suggest that the designed supramolecular nanovesicles could be successfully applied as nonviral gene delivery vectors.

Detailed chemical characterization and molecular modeling of serotonin inclusion complex with unmodified β-cyclodextrin

In this study, we analyzed the capability of unmodified β-cyclodextrin (β-CD) to form the stable complex with serotonin hydrochloride (SER), as an important neurotransmitter in the brain. The stable β-CD: SER formulation was prepared and characterized using spectroscopic, thermal, molecular docking, and molecular dynamics techniques, revealing the phenomenon of H-bond formations and the domination of hydrophobic forces between the host molecule and its guest via the amine group of SER and the narrow side of β-CD. The complexation mechanism was mainly enthalpy-driven, representing the improvement in SER photo-stability. Overall, the results highlighted the possibility to use this formulation with improved stability in clinical practice for treatment and prevention of various depressive conditions, such as anxiety disorders.

Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach

Efficient prediction and ranking of small molecule binders by their kinetic ( kon and koff) and thermodynamic ( Δ G) properties can be a valuable metric for drug lead optimization, as these quantities are often indicators of in vivo efficacy. We have previously described a hybrid molecular dynamics, Brownian dynamics, and milestoning model, Simulation Enabled Estimation of Kinetic Rates (SEEKR), that can predict kon's, koff's, and Δ G's. Here we demonstrate the effectiveness of this approach for ranking a series of seven small molecule compounds for the model system, β-cyclodextrin, based on predicted kon's and koff's. We compare our results using SEEKR to experimentally determined rates as well as rates calculated using long time scale molecular dynamics simulations and show that SEEKR can effectively rank the compounds by koff and Δ G with reduced computational cost. We also provide a discussion of convergence properties and sensitivities of calculations with SEEKR to establish "best practices" for its future use.